MITEs and small RNAs regulate genomic imprinting in the rice endosperm

ABSTRACT: Imprinting is an epigenetic phenomenon that describes unequal expression of paternal and maternal alleles in sexually reproducing organisms including mammals and flowering plants. In plants, imprinting occurs primarily in the endosperm, which provides nutrients for embryonic development in seeds and could potentially affect seed size and crop yield. The mechanism and effect of imprinted gene expression on seed development in crop plants are largely unknown. Genome-wide analyses of imprinted genes and small RNA loci in the endosperm of rice F1 reciprocal hybrids have identified 381 maternally expressed genes (MEGs), 21 paternally expressed genes (PEGs). 38 maternally expressed siRNA loci (MESRL), and 3 paternally expressed siRNA loci (PESRL). The overlap between imprinted genes and small RNA loci was low;16 MESRL and one PESRL were located in coding region of MEGs. Some MEGs were clustered, and several clusters were associated with long noncoding RNAs (lncRNAs). In comparison, 17% and 10% of MEGs in rice were conserved with those in maize and Arabidopsis, respectively. Interestingly, ~88% of MEGs were associated with miniature inverted-repeat transposable elements (MITEs) in the chromosome-arm regions. These MEGs with MITEs evolved faster than biparentally expressed genes. Most MEGs with MITEs generated 24-nucleotide (nt) small interfering RNAs (siRNAs) that are associated with methylation of paternal alleles. Furthermore, the MEGs contained candidate genes that are known to affect seed size and development in rice. Moreover, 103 MEGs are located within the QTL regions of 1000-kernel weight in rice. These data support a model that explains the parent-of-origin effect on gene expression and seed development of rice and other cereal crops. The 24-nt siRNAs could induce differential methylation between maternal and paternal alleles of the MITE-associated genes, leading to the expression of maternal alleles. The maternally expressed genes coincident with those genes and QTLs associated with seed size and development could be used to improve grain production of rice and other cereal crops. Overall design: mRNA and smallRNA profiling of two inbred lines of Oryza sativa L. susp. indica cv. Longtefu and O. sativa L. susp. japonica cv. 02428 and their reciprocal hybrids.

INSTRUMENT(S): Illumina HiSeq 2000 (Oryza sativa Japonica Group)

SUBMITTER: Jingya Yuan  

PROVIDER: GSE65137 | GEO |

SECONDARY ACCESSION(S): PRJNA273350

REPOSITORIES: GEO